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(-) Description

Title :  STRUCTURAL MODEL OF THE [FE]-HYDROGENASE/CYTOCHROME C553 COMPLEX COMBINING NMR AND SOFT-DOCKING
 
Authors :  X. Morelli, M. Czjzek, C. E. Hatchikian, O. Bornet, J. C. Fontecilla-Camps, N. P. Palma, J. J. G. Moura, F. Guerlesquin
Date :  13 Mar 00  (Deposition) - 25 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR; THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,D,E
Keywords :  Hydrogenase, Cytochrome C553, Electron Transfer Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Morelli, M. Czjzek, C. E. Hatchikian, O. Bornet, J. C. Fontecilla-Camps, N. P. Palma, J. J. Moura, F. Guerlesquin
Structural Model Of The Fe-Hydrogenase/Cytochrome C553 Complex Combining Transverse Relaxation- Optimized Spectroscopy Experiments And Soft Docking Calculations.
J. Biol. Chem. V. 275 23204 2000
PubMed-ID: 10748163  |  Reference-DOI: 10.1074/JBC.M909835199
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - [FE]-HYDROGENASE (LARGE SUBUNIT)
    Atcc: 7757
    Cellular Location: PERIPLASM
    Chains: A
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876
 
Molecule 2 - [FE]-HYDROGENASE (SMALL SUBUNIT)
    Atcc: 7757
    Cellular Location: PERIPLASM
    Chains: D
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876
 
Molecule 3 - CYTOCHROME C553
    Cellular Location: PERIPLASM
    Chains: E
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Theoretical Model (7, 12)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2CYN2Ligand/IonCYANIDE ION
3FE22Ligand/IonFE (II) ION
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5PDT1Ligand/Ion1,3-PROPANEDITHIOL
6SF43Ligand/IonIRON/SULFUR CLUSTER
7ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Theoretical Model (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPDT A:4 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , HOH A:11 , ALA A:293BINDING SITE FOR RESIDUE FE2 A 5
02AC2SOFTWAREPDT A:4 , FE2 A:5 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , HOH A:11 , PRO A:108 , THR A:145 , ALA A:149BINDING SITE FOR RESIDUE FE2 A 6
03AC3SOFTWAREHIS D:82 , LYS D:83 , HIS D:85 , ASP D:86BINDING SITE FOR RESIDUE ZN D 12
04AC4SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:8 , CMO A:9 , CMO A:10 , HOH A:11 , ALA A:149 , PRO A:203 , PHE A:296BINDING SITE FOR RESIDUE CYN A 7
05AC5SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CMO A:9 , CMO A:10 , HOH A:11 , PRO A:108 , ALA A:109 , ALA A:293 , THR A:294 , ILE A:295 , PHE A:296BINDING SITE FOR RESIDUE CYN A 8
06AC6SOFTWAREILE A:30 , LYS A:34 , CYS A:35 , ILE A:36 , GLY A:37 , CYS A:38 , ASP A:39 , CYS A:41 , SER A:42 , HIS A:58 , HIS A:75 , CYS A:76 , ILE A:81BINDING SITE FOR RESIDUE SF4 A 1
07AC7SOFTWAREVAL A:28 , TYR A:44 , CYS A:45 , CYS A:66 , ASN A:68 , CYS A:69 , GLY A:70 , CYS A:72BINDING SITE FOR RESIDUE SF4 A 2
08AC8SOFTWARECYS A:69 , CYS A:179 , PRO A:180 , CYS A:234 , LYS A:237 , MET A:376 , ALA A:377 , CYS A:378 , CYS A:382 , GLY A:385BINDING SITE FOR RESIDUE SF4 A 3
09AC9SOFTWAREFE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , ALA A:107 , PRO A:108 , ALA A:109 , VAL A:110 , LYS A:237 , ILE A:295 , PHE A:296 , GLY A:297BINDING SITE FOR RESIDUE PDT A 4
10BC1SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:10 , HOH A:11 , ALA A:107 , PRO A:108 , THR A:145 , PRO A:203BINDING SITE FOR RESIDUE CMO A 9
11BC2SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , HOH A:11 , ALA A:293 , THR A:294 , ILE A:295 , PHE A:296BINDING SITE FOR RESIDUE CMO A 10
12BC3SOFTWARECYS A:38 , GLY A:55 , CYS E:10 , CYS E:13 , HIS E:14 , MET E:23 , GLY E:24 , ALA E:26 , LYS E:27 , GLN E:32 , LEU E:37 , MET E:41 , TYR E:44 , TYR E:49 , GLY E:51 , GLU E:52 , ARG E:53 , MET E:56 , MET E:57 , TYR E:64BINDING SITE FOR RESIDUE HEM E 80

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E08)

(-) Cis Peptide Bonds  (7, 7)

Theoretical Model
No.Residues
1Leu A:131 -Ala A:132
2His A:141 -Cys A:142
3Cys A:142 -Trp A:143
4Met A:170 -Pro A:171
5Leu A:172 -Pro A:173
6Met A:391 -Pro A:392
7His D:91 -Trp D:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E08)

(-) PROSITE Motifs  (2, 3)

Theoretical Model (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.PHFL_DESVH26-57
59-86		  1-
A:59-86
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.PHFL_DESVH35-46
66-77		  2A:35-46
A:66-77

(-) Exons   (0, 0)

(no "Exon" information available for 1E08)

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:371
 aligned with PHFL_DESVH | P07598 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:371
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 
           PHFL_DESVH    27 FVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEA 397
               SCOP domains d1e08a_ A: [Fe]-hydrogenase/cytochrome c553 complex                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eee.....eee........................................eeeeee.......................................................................................................................eeeeee........................eee..........................................................................eee..eee..eee..eeee......................eee..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -            -4FE4S_FER_2  PDB: A:59-86   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------4FE4S_FER_1 -------------------4FE4S_FER_1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e08 A  27 FVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEA 397
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396 


Chain D from PDB  Type:PROTEIN  Length:88
 aligned with PHFS_DESVH | P07603 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:88
                                    45        55        65        75        85        95       105       115        
           PHFS_DESVH    36 VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE 123
               SCOP domains d1e08d_ D: [Fe]-hydrogenase/cytochrome c553 complex                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1e08 D  36 VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE 123
                                    45        55        65        75        85        95       105       115        


Chain E from PDB  Type:PROTEIN  Length:78
 aligned with CY553_DESVH | P04032 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:78
                                    35        45        55        65        75        85        95        
          CY553_DESVH    26 DGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL 103
               SCOP domains d1e08e_ E: [Fe]-hydrogenase/cytochrome c553 complex                            SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 1e08 E   2 DGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL  79
                                    11        21        31        41        51        61        71
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Theoretical Model
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1E08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E08)

(-) Gene Ontology  (10, 21)

Theoretical Model(hide GO term definitions)
Chain A   (PHFL_DESVH | P07598)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain D   (PHFS_DESVH | P07603)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain E   (CY553_DESVH | P04032)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1e08
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  CY553_DESVH | P04032
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  PHFL_DESVH | P07598
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  PHFS_DESVH | P07603
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CY553_DESVH | P04032: 1dvh 1dwl 2dvh
        PHFL_DESVH | P07598: 1gx7 1hfe
        PHFS_DESVH | P07603: 1gx7 1hfe

(-) Related Entries Specified in the PDB File

1dvh CYTOCHROME C553 (REDUCED) (NMR, 36 STRUCTURES)
1hfe HYDROGENASE 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS